RetrogeneDB ID: retro_ptro_2468

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:112128485..112129136(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: GSTM1
• Ensembl ID: ENSPTRG00000001061
• Aliases: None
• Description: glutathione S-transferase mu 1 [Source:HGNC Symbol;Acc:4632]

Sequence

>retro_ptro_2468
ATGCCCGTGACACTGGGGTACTGGGACATCTGAGGGCTGGCCCACGCCGTCTGCCTGCTCCTGCAATACACAGACTTAAG
CTATGAGGAAAAGAAGTACATGATGGGGTACGCTCCTGACTATGACAGAAGCCAGTGGCTGAATGAAAAATTCAAGCTGG
GCCTGGACTTTCCCAATCTGCCCTACTTGATTGATGGGGCTCACAAGATCACCCAGAGCAAGGCCATCCTGGGCTGCATT
GCCTACAAGCACAATCTGTGTGGGGAGACAGAAGGGGAGAAGATTTGGGAAGACATTTCGGAGAACCAGCTTGTGGACAA
CCACGTGCAGCTGGCCAGACTCTGCTACAACCCAGATTTTAAGAAACTGAAGCCAGAATACCTGGAGGCACTCCCTGCAA
TGCTGAAGCTCTACTCACAGTTTCTGGGGAAGCAGCCATGGTTTCTTGGGGACAAGATCACACTTGTGGATTTCATCGCG
TATGGTGTCCTTGAGAGAAACCAAGTATTTGAGCCCAAGTGGTTGGACGCCTTCCCAAACCTGAAGGACTTCATCTCCCG
ATTTGAGGGCTTGGAGATCTCTGCCTACATGAAATCCAGCTGCTTCCTCCCGAGACCTGTGTTCACAAAGATGGCTGTCT
GGGGCAACAAG

Alignment

ORF - retro_ptro_2468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPMTLGYWDIRGLAHAIRLLLEYTDSSYEEKKYSMGDAPDYDRSQWLNEKFKLGLDFPNLPYLIDGAHKI
          MP.TLGYWDI.GLAHA..LLL.YTD.SYEEKKY.MG.APDYDRSQWLNEKFKLGLDFPNLPYLIDGAHKI
Retrocopy MPVTLGYWDI*GLAHAVCLLLQYTDLSYEEKKYMMGYAPDYDRSQWLNEKFKLGLDFPNLPYLIDGAHKI

Parental  TQSNAILCYIARKHNLCGETEEEKICVDILENQTMDNHMQLGMICYNPEFEKLKPKYLEELPEKLKLYSE
          TQS.AIL..IA.KHNLCGETE.EKI..DI.ENQ..DNH.QL...CYNP.F.KLKP.YLE.LP..LKLYS.
Retrocopy TQSKAILGCIAYKHNLCGETEGEKIWEDISENQLVDNHVQLARLCYNPDFKKLKPEYLEALPAMLKLYSQ

Parental  FLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPNLKDFISRFEDLEKISAYMKSSRFLPRPVFT
          FLGK.PWF.G.KIT.VDF..Y.VL.....FEPK.LDAFPNLKDFISRFE.LE.ISAYMKSS.FLPRPVFT
Retrocopy FLGKQPWFLGDKITLVDFIAYGVLERNQVFEPKWLDAFPNLKDFISRFEGLE-ISAYMKSSCFLPRPVFT

Parental  KMAVWGNK
          KMAVWGNK
Retrocopy KMAVWGNK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.02 RPM	18.46 RPM
SRP007412_cerebellum	0.00 RPM	5.92 RPM
SRP007412_heart	0.00 RPM	1.87 RPM
SRP007412_kidney	0.05 RPM	9.89 RPM
SRP007412_liver	0.13 RPM	42.26 RPM
SRP007412_testis	0.00 RPM	12.54 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2468 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2468 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2468 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3643
Gorilla gorilla	retro_ggor_2459
Pongo abelii	retro_pabe_2990
Macaca mulatta	retro_mmul_1806
Callithrix jacchus	retro_cjac_2463

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003123	7 retrocopies	retro_cjac_1299, retro_cjac_2226, retro_cjac_2463, retro_cjac_2498, retro_cjac_3004, retro_cjac_3084, retro_cjac_811,
Gorilla gorilla	ENSGGOG00000005148	2 retrocopies	retro_ggor_1913, retro_ggor_2459,
Nomascus leucogenys	ENSNLEG00000003194	2 retrocopies	retro_nleu_1546, retro_nleu_504,
Pongo abelii	ENSPPYG00000001064	2 retrocopies	retro_pabe_2218, retro_pabe_2990,
Pan troglodytes	ENSPTRG00000001061	2 retrocopies	retro_ptro_1859, retro_ptro_2468 ,
Pan troglodytes	ENSPTRG00000001063	2 retrocopies	retro_ptro_1393, retro_ptro_1709,